PRIDE Database

Overview

The PRIDE Archive (ProteomicsIDEntifications database) at EMBL-EBI is the world's largest public mass-spectrometry proteomics repository — 39,000+ projects and 3.4M+ deposited files as of 2026. Programmatic access is via a JSON REST API at https://www.ebi.ac.uk/pride/ws/archive/v3/. No authentication is required. The OpenAPI/Swagger spec is at https://www.ebi.ac.uk/pride/ws/archive/v3/v3/api-docs. PRIDE v3 returns plain JSON arrays for list endpoints (no HAL+JSON _embedded envelope) and intentionally does not expose per-peptide or per-PSM identification endpoints — for spectrum-level identifications, download the project's RESULT files (mzIdentML, MaxQuant txt, etc.) and parse them locally.

When to Use

• Finding published proteomics datasets by free-text keyword and facet filters (organism, tissue, disease, instrument, software, PTM) for meta-analysis or benchmarking
• Downloading raw mass-spectrometry data (RAW, mzML, MGF) or pre-processed identifications (RESULT files) from a specific PRIDE project accession
• Looking up which PRIDE projects mention a specific UniProt protein accession (project-level occurrence map only — no PSM/coverage counts at the API surface)
• Finding similar projects to one of interest for reanalysis or cross-study comparison
• Fetching SDRF (Sample-Data Relationship Format) files for projects so you can model the sample-to-MS-run mapping programmatically
• Discovering valid filter values via faceted search before constructing a structured query
• For protein sequences, Swiss-Prot annotations, and ID mapping use uniprot-protein-database
• For protein domain and family classification use interpro-database — PRIDE only reports project-level occurrence, not domain-level features
• PRIDE v3 has no /peptides, /psms, or /proteins?proteinAccession= endpoints — if you need peptide- or PSM-level data, download the RESULT files from /projects/{accession}/files and parse them with pyteomics or a search-engine-specific reader

Prerequisites